<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>1 apr 2012 kl. 15.16 skrev Roland Schulz:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><br><div class="gmail_quote">On Sun, Apr 1, 2012 at 9:09 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">On 2012-04-01 15:05, Roland Schulz wrote:<br>
><br>
><br>
> On Sun, Apr 1, 2012 at 6:20 AM, David van der Spoel<br>
</div><div><div class="h5">> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>>> wrote:<br>
><br>
> On 2012-04-01 05:50, Shirts, Michael (mrs5pt) wrote:<br>
> > Hi, all-<br>
> ><br>
> > I'm very recently (with 4.6 updates in the last couple of weeks)<br>
> having<br>
> > issues with building gromacs with threads on OS X. When I try to<br>
> compile<br>
> > with shared libraries, I get:<br>
> ><br>
> > ld: warning: in /usr/local/lib/libgomp.dylib, file was built for<br>
> i386 which<br>
> > is not the architecture being linked (x86_64)<br>
> ><br>
> > When I build without shared libraries, it compiles, but crashes<br>
> when run<br>
> > with -nt more than 1.<br>
> ><br>
> > Currently using OS X 10.6.8, gcc 4.1.2 to compile.<br>
> ><br>
> > Everything works fine with 4.5.5, and with earlier versions of 4.6.<br>
> ><br>
> > Anyone else having similar problems, or know what changes could<br>
> have caused<br>
> > this?<br>
><br>
> There is a redmine for this (900).<br>
><br>
><br>
> Michael's issue is a different because it is gcc 4.1.2 and because it is<br>
> not a segfault but the linker errorr.<br>
> I'm surprised that you get a linker error. gcc 4.1 doesn't support<br>
> OpenMP and if run cmake with gcc 4.1 on Linux I get:<br>
> Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)<br>
<br>
</div></div>He does mention a crash with -nt > 1, and it is only recently, he also<br>
links to libgomp, so it must be the same error.<br></blockquote><div><br></div><div>True. I overlooked that part. Yes that part is the same. I'm still puzzled why cmake doesn't detect that gcc 4.1 doesn't have OpenMP. </div></div></blockquote><div><br></div><div>From Red Hat a flavor of gcc 4.1.2 once emerged that supported OpenMP. Some other distros picked it up, so although the standard gcc didn't get OpenMP support until later, 4.1.2 is not necessarily non-OpenMP. Apples gcc could furthermore very well be modified in similar ways.</div><div><br></div><div>Erik</div><br><blockquote type="cite"><div class="gmail_quote">
<div>@Michael: Or was your compiler version a typo and you are also using gcc 4.2?</div><div><br></div><div>Roland</div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
><br>
> If you rerun cmake (without a cache), do you still not get any error<br>
> during cmake?<br>
><br>
> BTW: We probably should automatic disable OpenMP if the flags can't be<br>
> found (e.g. for clang and gcc <4.2)<br>
<br>
</div>At least on Macs for now.<br>
<div class="im"><br>
><br>
> Roland<br>
><br>
><br>
> Your simplest solution is cmake -DGMX_OPENMP:BOOL=OFF<br>
><br>
> ><br>
> > Thanks!<br>
> > ~~~~~~~~~~~~<br>
> > Michael Shirts<br>
> > Assistant Professor<br>
> > Department of Chemical Engineering<br>
> > University of Virginia<br>
</div>> > <a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a> <mailto:<a href="mailto:michael.shirts@virginia.edu">michael.shirts@virginia.edu</a>><br>
> > <a href="tel:%28434%29-243-1821" value="+14342431821">(434)-243-1821</a> <tel:%28434%29-243-1821><br>
<div class="im">> ><br>
><br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205">+46184714205</a><br>
</div>> <tel:%2B46184714205>.<br>
> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>><br>
<div class="im">> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
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><br>
><br>
><br>
><br>
><br>
><br>
<span class="HOEnZb"><font color="#888888">><br>
> --<br>
> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov/" target="_blank">cmb.ornl.gov</a> <<a href="http://cmb.ornl.gov/" target="_blank">http://cmb.ornl.gov</a>><br>
</font></span><div class="im HOEnZb">> <a href="tel:865-241-1537" value="+18652411537">865-241-1537</a>, ORNL PO BOX 2008 MS6309<br>
><br>
><br>
<br>
<br>
</div><div class="HOEnZb"><div class="h5">--<br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se/" target="_blank">http://folding.bmc.uu.se</a><br>
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</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov/">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
-- <br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-developers-request@gromacs.org.</blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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